loci.formats.IFormatReader Java Examples

public Point[] getTileIndices(IFormatReader reader, int tileWidth, int tileHeight) {
    Rectangle region = new Rectangle(0, 0, reader.getSizeX()+1, reader.getSizeY() + 1);
    int minTileX = XToTileX(region.x,0,tileWidth);
    int maxTileX = XToTileX(region.x + region.width - 1,0,tileWidth);
    int minTileY = this.YToTileY(region.y,0,tileHeight);
    int maxTileY = this.YToTileY(region.y + region.height - 1,0,tileHeight);
    Point[] tileIndices = new Point[(maxTileY - minTileY + 1) * (maxTileX - minTileX + 1)];
    int tileIndexOffset = 0;

    for(int ty = minTileY; ty <= maxTileY; ++ty) {
        for(int tx = minTileX; tx <= maxTileX; ++tx) {
            tileIndices[tileIndexOffset++] = new Point(tx, ty);
        }
    }

    return tileIndices;
}
 

@Deprecated
private int getRealResolutionCount(IFormatReader imageReader) throws IOException, FormatException {
    ImageReader ir = new ImageReader();
    ir.setFlattenedResolutions(false);
    ir.setId(imageReader.getCurrentFile());
    ir.setSeries(imageReader.getSeries());
    int numRes = 1;
    for (int lev=imageReader.getResolutionCount()-1; lev>=0; lev--) {
        numRes = lev;
        ir.setResolution(lev);
        int thumbW = ir.getSizeX();
        int thumbH = ir.getSizeY();
        double diff = Math.abs((thumbW/(double)thumbH) - (imageReader.getSizeX()/(double)imageReader.getSizeY()));
        System.out.println("diff: "+diff);
        if (diff<0.001) break;
    }
    ir.close();
    return numRes;
}
 

private IFormatReader getIFormatReader(String filename, final OrbitModel orbitModel) {
    IFormatReader r;
    if (filename.toLowerCase().endsWith("ndpis")) {
        r = new NDPISReaderOrbit();
        if (orbitModel!=null) {
            // mIHC demuxing active?
            if (orbitModel.getFeatureDescription().isMihcActive()) {
                try {
                    BufferedImageReader bir = new BufferedImageReader(r);
                    bir.setId(filename);
                    double[] gains = NDPIUtils.getExposureTimesGain((NDPISReaderOrbit) r);
                    r.close();
                    MihcConfig mihcConfig = new MihcConfig(orbitModel.getFeatureDescription().getMihcMatrixChannelNames(),orbitModel.getFeatureDescription().getMihcMatrix(),orbitModel.getFeatureDescription().getMihcNormalGain());
                    r = new MultiplexImageReader(bir,mihcConfig,gains);
                    logger.info("multiplex reader used");
                } catch (Exception e) {
                    e.printStackTrace();
                } 
            }
        }
    } else if (filename.toLowerCase().endsWith("ndpi")) {
        // this check will become unnecessary when this bug is fixed: https://github.com/ome/bioformats/issues/3544
        // could then just use ImageReader() and allow it to auto-detect.
        r = new NDPIReader();
    } else {
        r = new ImageReader();
    }
    // r.setAllowOpenFiles(true);
    r.setFlattenedResolutions(false);
    return r;
}
 

@Override
public void close() throws IOException {
    synchronized (allReaders) {
        for (IFormatReader r: allReaders) {
            try {
                r.close();
            } catch (Exception e) {
            }
        }
    }
}
 

public BufferedImage getThumbnail() {
  //  if (true) return new BufferedImage(100,60,BufferedImage.TYPE_INT_RGB);
     long thumbW=1;
     long thumbH=1;

    try {
        IFormatReader ir = getIFormatReader(reader.get().getCurrentFile(),null);
        ir.setId(reader.get().getCurrentFile());
        ir.setSeries(reader.get().getSeries());

        //int lev = numLevels-1;
        for (int lev=numLevels-1; lev>=0; lev--)
        {
            ir.setResolution(lev);
            thumbW = ir.getSizeX();
            thumbH = ir.getSizeY();
            double diff = Math.abs((thumbW/(double)thumbH) - (width/(double)height));
            logger.trace("thumb lev: "+lev+"  diff: "+diff+"  WxH: "+thumbW+"x"+thumbH);
            if (diff< THUMBNAIL_RATIO_DIFF) break; // 0.001
        }

        BufferedImageReader bir = BufferedImageReader.makeBufferedImageReader(ir);
        BufferedImage thumb = bir.openImage(0);
        bir.close();

        if (thumbW>maxThumbWidth) {
            int h = (int)(maxThumbWidth * (thumbH/(double)thumbW));
            BufferedImage img = new BufferedImage(maxThumbWidth,h, BufferedImage.TYPE_INT_RGB);
            Graphics2D g2d = (Graphics2D) img.getGraphics();
            g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
            g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR);
            g2d.drawImage(thumb,0,0,maxThumbWidth,h, null);
            thumb = img;
        }
        return thumb;
    } catch (IOException | FormatException e) {
        e.printStackTrace();
    }
    return null;
}
 

@Deprecated
private int getIndex(IFormatReader r, int channel) {
    int[] nos = r.getZCTCoords(0);
    int z = nos[0], t = nos[2];
    return r.getIndex(z,channel,t);
}
 

private boolean doMergeChannels(IFormatReader r) {
  // return !r.isRGB();
   int c = r.getSizeC();
   return c > 1 && !r.isRGB();
}
 

public static final double[] getPlanePosition( final IFormatReader r, final MetadataRetrieve retrieve, int series, int t )
{
	return getPlanePosition(r, retrieve, series, t, false, false, false);
}
 

private static void printMetaData( final IFormatReader r )
{
	printMetaData( r.getGlobalMetadata() );
}
 

public static void printMetaData( final IFormatReader r )
{
	printMetaData( r.getGlobalMetadata() );
}
 

public static IFormatReader instantiateImageReader()
{
	// should I use the ZeissCZIReader here directly?
	return new ChannelSeparator();// new ZeissCZIReader();
}
 

public static IFormatReader instantiateImageReader()
{
	// should I use the ZeissCZIReader here directly?
	return new ChannelSeparator();// new ZeissCZIReader();
}
 

public IFormatReader getReader() { return r; } 

public IFormatReader getReader() { return r; }